How DNA Evidence Works

Introduction to How DNA Evidence Works

The CBS drama "CSI: Crime Scene Investigation" routinely draws more than 20 million viewers per episode, making it one of television's greatest successes. The show's popularity owes a great deal to the writers and actors who bring the stories to life. But another intriguing element is the cutting-edge technology used by the Las Vegas crime lab trying to solve crimes. Collecting and analyzing DNA evidence tops the list of the lab's forensic toolkit, and its ubiquity in shows like "CSI" and "Cold Case" has increased public awareness to the point that many jurors in real-world courtrooms expect to see DNA evidence presented -- whether a case calls for it or not.

It's hard to believe that DNA evidence has come so far so fast. The techniques that make it possible to identify a suspect using his or her unique genetic blueprint have only been around since 1985. That's when Alec Jeffreys and his colleagues in England first demonstrated the use of DNA in a criminal investigation. Since then, DNA evidence has played a bigger and bigger role in many nations' criminal justice systems. It has been used to prove that suspects were involved in crimes and to free people who were wrongly convicted. And, in the United States, it has been integral to several high-profile criminal cases.

At the heart of DNA evidence is the biological molecule itself, which serves as an instruction manual and blueprint for everything in your body (see How Cells Work for details). A DNA molecule is a long, twisting chain known as a double helix. DNA looks pretty complex, but it's really made of only four nucleotides:

Adenine

Cytosine

Guanine

Thymine

These nucleotides exist as base pairs that link together like the rungs in a ladder. Adenine and thymine always bond together as a pair, and cytosine and guanine bond together as a pair. While the majority of DNA doesn't differ from human to human, some 3 million base pairs of DNA (about 0.10 percent of your entire genome) vary from person to person.

In human cells, DNA is tightly wrapped into 23 pairs of chromosomes. One member of each chromosomal pair comes from your mother, and the other comes from your father. In other words, your DNA is a combination of your mother's and your father's DNA. Unless you have an identical twin, your DNA is unique to you.

This is what makes DNA evidence so valuable in investigations -- it's almost impossible for someone else to have DNA that is identical to yours. But catching a criminal using DNA evidence is not quite as easy as "CSI" makes it seem, as this article will demonstrate. Our first step in exploring DNA evidence is the crime scene -- and the biological evidence gathered there by detectives.

Collecting DNA Evidence

For many years, fingerprints were the gold standard for linking suspects to a crime scene. Today, the gold standard is DNA evidence because DNA can be collected from virtually anywhere. Even a criminal wearing gloves may unwittingly leave behind trace amounts of biological material. It could be a hair, saliva, blood, semen, skin, sweat, mucus or earwax. All it takes is a few cells to obtain enough DNA information to identify a suspect with near certainty.

For this reason, law enforcement officials take unusual care at crime scenes. Police officers and detectives often work closely with laboratory personnel or evidence collection technicians to make sure evidence isn't contaminated. This involves wearing gloves and using disposable instruments, which can be discarded after collecting each sample. While collecting evidence, officers are careful to avoid touching areas where DNA evidence could exist. They also avoid talking, sneezing and coughing over evidence or touching their face, nose or mouth.

The following list shows some common sources of DNA evidence:

A weapon, such as a baseball bat, fireplace poker or knife, which could contain sweat, skin, blood or other tissue

A hat or mask, which could contain sweat, hair or dandruff

A facial tissue or cotton swab, which could contain mucus, sweat, blood or earwax

A toothpick, cigarette butt, bottle or postage stamp, all of which could contain saliva

A used condom, which could contain semen or vaginal or rectal cells

Bed linens, which could contain sweat, hair, blood or semen

A fingernail or partial fingernail, which could contain scraped-off skin cells

When investigators find a piece of evidence, they place it in a paper bag or envelope, not in a plastic bag. This is important because plastic bags retain moisture, which can damage DNA. Direct sunlight and warmer conditions may also damage DNA, so officers try to keep biological materials at room temperature. They label the bags with information about what the material is, where it was found and where it will be transported. These are chain-of-custody procedures, which ensure the legal integrity of the samples as they move from collection to analysis.

Analysis occurs in a forensic laboratory, the topic of our next section.

DNA Analysis: Traditional Techniques

From the crime scene, a piece of DNA evidence travels to a forensic laboratory. These labs vary quite a bit, both in terms of how they are structured and what kind of analyses they offer. Public laboratories are often associated with a law enforcement entity or the district attorney's office, while others are independent government entities. Private forensic laboratories, some dedicated just to DNA analysis, also exist.

Many labs have the ability to conduct testing on nuclear DNA, which is the copy of DNA that exists in the nucleus of every cell. But only a few labs offer more specialized techniques, such as Y-chromosome or mitochondrial DNA analysis. Let's look at some of these techniques in greater detail.

Restriction fragment length polymorphism (RFLP) analysis was one of the first forensic methods used to analyze DNA. It analyzes the length of strands of DNA that include repeating base pairs. These repetitions are known as variable number tandem repeats (VNTRs) because they can repeat themselves anywhere from one to 30 times.

RFLP analysis requires investigators to dissolve DNA in an enzyme that breaks the strand at specific points. The number of repeats affects the length of each resulting strand of DNA. Investigators compare samples by comparing the lengths of the strands. RFLP analysis requires a fairly large sample of DNA that hasn't been contaminated with dirt.

Many laboratories are replacing RFLP analysis with short tandem repeat (STR) analysis. This method offers several advantages, but one of the biggest is that it can start with a much smaller sample of DNA. Scientists amplify this small sample through a process known as polymerase chain reaction, or PCR. PCR makes copies of the DNA much like DNA copies itself in a cell, producing almost any desired amount of the genetic material.

Once the DNA in question has been amplified, STR analysis examines how often base pairs repeat in specific loci, or locations, on a DNA strand. These can be dinucleotide, trinucleotide, tetranucleotide or pentanucleotide repeats -- that is, repetitions of two, three, four or five base pairs. Investigators often look for tetranucleotide or pentanucleotide repeats in samples that have been through PCR amplification because these are the most likely to be accurate.

The Federal Bureau of Investigation (FBI) has chosen 13 specific STR loci to serve as the standard for DNA analysis. The likelihood that any two individuals (except identical twins) will have the same 13-loci DNA profile can be as high as 1 in 1 billion or greater.

DNA Analysis: Specialized Techniques

Although most labs use either RFLP or STR techniques for their DNA analysis, there are situations that require a different approach. One such situation is when there are multiple male contributors of genetic material, which sometimes happens in sexual assault cases. The best way to resolve the complex mixture and sort out exactly which men were involved is Y-marker analysis. As its name suggests, this technique examines several genetic markers found on the Y chromosome. Because the Y chromosome is transmitted from a father to all his sons, DNA on the Y chromosome can be used to identify DNA from different males. Y-marker analysis can also be used to trace family relationships among males.

Another situation involves identifying old remains or biological evidence lacking nucleated cells, such as hair shafts, bones and teeth. RFLP and STR testing can't be used on these materials because they require DNA found in the nucleus of a cell. In these cases, investigators often use mitochondrial DNA (mtDNA) analysis, which uses DNA from a cell's mitochondria. Investigators have found mtDNA testing to be very useful in solving cold cases, which are murders, missing-person cases or suspicious deaths that are not being actively investigated. Cold cases often have biological evidence in the form of blood, semen and hair that has been stored for a long time or improperly stored. Submitting those degraded samples for mtDNA testing can sometimes break the case open and help detectives find the perpetrator.

A relatively new technique -- SNP analysis -- is also useful in certain cases where forensic labs are presented with highly degraded DNA samples. This technique requires that scientists analyze variations in DNA where one nucleotide replaces another. Such a genetic change is called a single nucleotide polymorphism, or SNP (pronounced "snip"). SNPs make excellent markers and are most often used to determine a person's susceptibility to a certain disease. But forensics labs turn to SNP analysis on occasion. For example, forensic scientists used SNP technology successfully to identify several Sept. 11 World Trade Center victims for whom other methods had failed.

In reality, analyzing a DNA sample is just a first step. Up next, we'll take a look at what happens after the analysis is complete.

DNA evidence is now as important as fingerprints in convicting criminals and freeing innocent suspects.

Matching DNA

The main objective of DNA analysis is to get a visual representation of DNA left at the scene of a crime. A DNA "picture" features columns of dark-colored parallel bands and is equivalent to a fingerprint lifted from a smooth surface. To identify the owner of a DNA sample, the DNA "fingerprint," or profile, must be matched, either to DNA from a suspect or to a DNA profile stored in a database.

Let's consider the former situation -- when a suspect is present. In this case, investigators take a DNA sample from the suspect, send it to a lab and receive a DNA profile. Then they compare that profile to a profile of DNA taken from the crime scene. There are three possible results:

Inclusions -- If the suspect's DNA profile matches the profile of DNA taken from the crime scene, then the results are considered an inclusion or nonexclusion. In other words, the suspect is included (cannot be excluded) as a possible source of the DNA found in the sample.

Exclusions -- If the suspect's DNA profile doesn't match the profile of DNA taken from the crime scene, then the results are considered an exclusion or noninclusion. Exclusions almost always eliminate the suspect as a source of the DNA found in the sample.

Inconclusive results -- Results may be inconclusive for several reasons. For example, contaminated samples often yield inconclusive results. So do very small or degraded samples, which may not have enough DNA to produce a full profile.

Sometimes, investigators have DNA evidence but no suspects. In that case, law enforcement officials can compare crime scene DNA to profiles stored in a database. Databases can be maintained at the local level (the crime lab of a sheriff's office, for example) or at the state level. A state-level database is known as a State DNA index system (SDIS). It contains forensic profiles from local laboratories in that state, plus forensic profiles analyzed by the state laboratory itself. The state database also contains DNA profiles of convicted offenders. Finally, DNA profiles from the states feed into the National DNA Index System (NDIS).

To find matches quickly and easily in the various databases, the FBI developed a technology platform known as the Combined DNA Index System, or CODIS. The CODIS software permits laboratories throughout the country to share and compare DNA data. It also automatically searches for matches. The system conducts a weekly search of the NDIS database, and, if it finds a match, notifies the laboratory that originally submitted the DNA profile. These random matches of DNA from a crime scene and the national database are known as "cold hits," and they are becoming increasingly important. Some states have logged thousands of cold hits in the last 20 years, making it possible to link otherwise unknown suspects to crimes.

DNA evidence can pinpoint whether or not someone is a parent.

Photo courtesy Genelex, Inc

Using DNA Evidence Beyond the Courtroom

DNA evidence plays a pivotal role in the modern criminal justice system, but the same techniques that prove guilt or exonerate an innocent person are just as useful outside the courtroom. Here are a few examples:

Paternity testing and other cases where authorities need to prove whether individuals are related or not -- One of the more infamous paternity cases of late occurred after Anna Nicole Smith's death in 2007. Five different men claimed to be the father of Smith's baby daughter, Dannielynn. After a DNA test, Larry Birkhead was proven to be the child's father.

Identification of John or Jane Does -- Police investigators often face the unpleasant task of trying to identify a body or skeletal remains. DNA is a fairly resilient molecule, and samples can be easily extracted from hair or bone tissue. Once a DNA profile has been created, it can be compared to samples from families of missing persons to see if a match can be made. The military even uses DNA profiles in place of the old-school dog tag. Each new recruit must provide blood and saliva samples, and the stored samples can subsequently be used as a positive ID for soldiers killed in the line of duty. Even without a DNA match to identify a body conclusively, a profile is useful because it can provide important clues about the victim, such as his or her sex and race.

Studying the evolution of human populations -- Scientists are trying to use samples extracted from skeletons and from living people around the world to show how early human populations might have migrated across the globe and diversified into so many different races. In the 1980s, scientists at the University of California, Berkeley, used mitochondrial DNA analysis to speculate that all living humans are related to a single woman -- "Eve" -- who lived roughly 150,000 years ago in Africa. Other scientists, using increasingly more sensitive DNA analysis, have since confirmed this to be true.

Studying inherited disorders -- Scientist also study the DNA fingerprints of families with members who have inherited diseases like Alzheimer's disease to try to ferret out chromosomal differences between those without the disease and those who have it, in the hope that these changes might be linked to getting the disease. DNA testing can also reveal a person's susceptibility to certain diseases. Several companies, such as 23andMe, deCODEme and Navigenics, offer at-home genetics tests that can evaluate your risk for hundreds of diseases and traits, including breast cancer, rheumatoid arthritis and Type 2 Diabetes.

Catching poachers -- Wildlife biologists are now turning to DNA tests to catch people who hunt illegally. For example, the hunting season for doe on public lands lasts only two days in many states. If a wildlife official suspects a hunter has shot a female deer after the official close of the season, he can analyze DNA from the meat and determine the species and gender of the animal.

Clarifying history -- Historians are turning to DNA evidence to learn more about the past. For example, Y-chromosome testing was used in 1998 to determine whether Thomas Jefferson, the third president of the United States, fathered children with one of his slaves or not. And in May 2009, a group of historians asked a Philadelphia museum if they could have access to a strip of a pillowcase stained with the blood of Abraham Lincoln. Their goal was to analyze Lincoln's DNA to see if he suffered from a rare genetic cancer syndrome called multiple endocrine neoplasia type 2B, but the museum's board would not allow the test at the time.

Privacy Concerns

Several countries, including the United States and Britain, have built elaborate databases with hundreds of thousands of unique individual DNA profiles. However, these databases also raise questions about privacy. DNA holds a lot more information about a person than fingerprints do. For example, a person's DNA includes information about everything from eye color to genetic defects. Some people fear that the widespread use of DNA databases could encourage governments to discriminate against people because of information encoded in their DNA. However, the DNA analyzed by the FBI's CODIS software is not currently thought to correlate to a person's actual traits.

Limitations of DNA Evidence

DNA evidence is powerful, but it does have limitations. One limitation is related to misconceptions about what a DNA match really means. Matching DNA from a crime scene to DNA taken from a suspect is not an absolute guarantee of the suspect's guilt. Instead, forensic experts prefer to talk about probability. For example, they might make a statement like this: The chance is 1/7,000 that an unrelated person would by chance have the same DNA profile as that obtained from the evidence. Combine that statistical analysis with other evidence, and you can see how prosecutors can make strong cases against a suspect.

A contributing factor to public misconception is how DNA analysis is portrayed in movies and television. Some lawyers and judges complain that a so-called "CSI effect" is influencing criminal justice. The CSI effect manifests itself when jurors demand DNA tests in cases where they are unnecessary or rely too heavily on DNA evidence to the exclusion of other physical evidence taken at a crime scene.

Even more troubling are cases of DNA fraud -- instances where criminals plant fake DNA samples at a crime scene. In 1992, Canadian physician John Schneeberger planted fake DNA evidence in his own body to avoid suspicion in a rape case. Planting fake DNA obtained from someone else is only part of the problem. Scientists at Nucleix, an Israeli company, recently reported that they could, with access to profiles stored in one of the DNA databases, manufacture a sample of DNA without obtaining any tissue from that person.

Nucleix has developed a test to distinguish real DNA samples from fake ones, with the goal of selling the test to forensic laboratories. But taking these extra precautions to ensure the validity of its results will only slow down busy labs even more. In fact, forensic casework backlogs are becoming a serious problem. A study conducted by the Bureau of Justice Statistics found that more than half a million cases were backlogged in forensic labs, which means felons and other violent offenders could be walking the streets while their DNA evidence sits in a queue, waiting to be tested [source: Houck].

As advances in DNA testing are made, some of these challenges may become less severe. But other, unforeseen challenged will likely emerge. Up next, we'll examine some of these advances and their implications.

Larry Birkhead was one of at least three men claiming to be the father of Anna Nicole Smith's baby, Danielynn. DNA results ultimately revealed Birkhead to be the biological father.

Advances in DNA Evidence

In 1985, DNA entered the courtroom for the first time as evidence in a trial, but it wasn't until 1988 that DNA evidence actually sent someone to jail. This is a complex area of forensic science that relies heavily on statistical predictions. In early cases where jurors were hit with reams of evidence heavily laden with mathematical formulas, it was easy for defense attorneys to create doubt in jurors' minds. Since then, a number of advances have allowed criminal investigators to perfect the techniques involved and face down legal challenges to DNA fingerprinting. Improvements include:

Source of DNA -- Science has devised ingenious ways of extracting DNA from sources that used to be too difficult or too contaminated to use. And in some cases, detectives are using DNA analysis in ingenious ways to get a conviction. For example, detectives in Phoenix, Ariz., were able to link a suspect to a murder victim by testing the DNA of a palo verde tree found at the crime scene. Palo verde trees feature pods containing seeds. Some of these pods were found in the suspect's truck. To prove that the pods came from the tree found at the crime scene and not some other palo verde tree, detectives turned to DNA analysis. The pods found in the truck matched each other -- and matched the pods taken from the tree at the crime scene. It was the first time the DNA fingerprint of a plant was used in a criminal trial.

Expanded DNA databases -- The databases managed by the CODIS software continue to expand. Prior to 2006, only convicted felons were required to have their DNA profiles entered into the database. But a January 2006 law, which was signed by President Bush and funded in 2008, has expanded collection of DNA samples beyond convicts to include federal arrestees, as well as suspected illegal immigrants or captives in the war on terrorism. Justice officials estimate the new collecting requirements will add DNA from an additional 1.2 million people to the database each year [source: UPI].

Training -- Crime labs have developed formal protocols for handling and processing evidence, reducing the likelihood of contamination of samples. On the courtroom side, prosecutors have become savvier at presenting genetic evidence, and many states have come up with specific rules governing its admissibility in court cases. See How CSI Works for more details.

The advances that have made DNA evidence an invaluable tool in the criminal justice system have also galvanized public interest. Classroom study of DNA and its properties has become more in-depth and widespread in many schools. And television crime dramas that feature DNA evidence so prominently continue to flourish. All of that awareness brings good news and bad news, but the real bad news is reserved for criminals, who will find it increasingly difficult to leave a crime scene without leaving a piece of incriminating biological evidence behind.